I acquired a batch of images with exactly the same settings using a Nikon C2 confocal system in the past month and a fixed pixel to micron ration for all of them -- independently of channels. However, when I read my .nd2 files using Bio-Formats plugin, sometimes the Pixel width value doesn't match the Pixel height.
Hence, it affects when using analysis tools such as "Analyze particles" and when saving the images from individual channels as tifs, jpegs, etc.
Interestingly, for some of the images the values that appear are the correct ones, for others it varies from 2.618 to 2.625, even though all the acquisitions were performed with the same settings. It is important to note that Nikon elements shows the same values for for pixel height and width, regardless of what is read on Fiji.
I know from my acquisition parameters that the Pixel height value is the correct one, and it is possible to fix the problem by inputting the appropriate value in the image properties. Nevertheless, I was wondering if you have any idea about why this is happening and if there is a package out there that can automatically fix it.
Thanks for the help,